Biology subjects

Jones, E.

Publications and source records attributed to Jones, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Selective Nerve Block of A- or C-Afferents Confirms Dual Role in Touch Pleasantness but Not Touch-Pain Modulation

Gentle and deep pressure are distinct types of touch that often elicit pleasant sensations and modulate pain. Although touch pleasantness has traditionally been attributed to unmyelinated C-tactile afferents, growing evidence suggests an important contribution of myelinated A-fibers. However, the relative role of A- and C-fibers in touch-evoked pleasantness and pain modulation remains unclear. To test the role of A- and C-fibers in touch pleasantness, healthy adults underwent selective peripheral nerve block of the superficial radial nerve to preferentially impair either A- or C-fiber function. Touch pleasantness of brushing (Study 1; N = 24) or deep pressure (Study 2; N = 24) and touch-induced modulation of heat pain were assessed before and after the nerve block. Both nerve blocks significantly reduced the perceived pleasantness of both gentle brushing and deep pressure, supporting a substantial contribution of myelinated A-fibers and well as unmyelinated C-fibers (presumably C-tactile fibers) to affective touch. In addition, block of A-fibers did not diminish touch-induced modulation of experimental heat pain, suggesting a particular pain-inhibiting role for C-tactile fibers. These findings supply causal evidence in healthy adults that myelinated A-fibers are highly involved in touch pleasantness-alongside C-tactile fibers-but are not involved in touch-induced pain relief.

neuroscience↗

bioRxiv2026

Neural feature spaces: characterizing the geometry of brain activity across development

The human brain undergoes profound changes from childhood to adulthood. These changes are foundational to cognitive, affective and social development, and measuring them is essential for identifying atypical development. A common approach consists of analyzing metrics derived from brain activity, such as spectral power, aperiodic activity and signal complexity. However, individual metrics are sensitive to external factors unrelated to development, contributing to inconsistent findings in the literature. Moreover, these metrics are not independent; they show some degree of intrinsic redundancy, which itself evolves across development. Here, we propose a novel approach that focuses on the relationships between neural features rather than their values, defining a "neural feature space" that captures the geometry of brain activity. We analyzed the neural feature spaces of children (4-12 years) and adults (30-45 years), based on 128-channel EEG recordings during naturalistic movie viewing. Specifically, we computed a range of spectral, aperiodic and complexity features and quantified pairwise distances between them using latent variable modeling. Neural feature spaces were significantly different between age groups. Notably, high frequency bands were less differentiated in children and distances between spectral and complexity features differed. Crucially, distances were highly stable across tasks, in contrast to feature values, which varied substantially. These findings suggest that the geometry of neural feature spaces provides robust, interpretable markers of neurodevelopment, offering a complementary approach to feature-based analyses.

neuroscience↗

bioRxiv2026

Global identification of neuronal and astrocytic integral membrane proteins that require Retromer for their endosomal recycling.

Efficient transport of membrane proteins through the endosomal network is essential for brain development and function, with perturbation implicated in disease. Deficiencies in Retromer, a key regulator of endosomal transport, have been linked to aging-related neurodegenerative disorders including Alzheimers and Parkinsons disease. To better define the neuroprotective role of Retromer, we have applied cell surface restricted proteomics to identify those integral membrane proteins whose recycling to the plasma membrane is mediated by Retromer and associated cargo adaptors, sorting nexin 3 (SNX3), its paralogue sorting nexin 12 (SNX12), and sorting nexin 27 (SNX27) (data available via ProteomeXchange: PXD078277). By comparing primary rat cortical neurons and astrocytes we have identified several cargoes that require either SNX3/SNX12- or SNX27-Retromer complexes for endosomal recycling, including proteins involved in synapse organisation, synaptic signalling and Alzheimers disease pathology. We highlight that perturbed Retromer function leads to endosomal enlargement, and we establish a key role of SNX27-Retromer in modulating transport of glutamate across both neuronal and astrocytic membranes via recycling of glutamate transporters EAAT3 (SLC1A1) and EAAT1 (SLC1A3) respectively. Our study provides further mechanistic insight into the consequences of Retromer deficiency for neuronal and astrocytic function, offering new avenues of research in the treatment of neurodegenerative disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/724903v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@1225eedorg.highwire.dtl.DTLVardef@1863f1dorg.highwire.dtl.DTLVardef@99c21eorg.highwire.dtl.DTLVardef@976bfd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Suppression of Retromer and the sorting nexins (SNX27, SNX3/SNX12) leads to a significant change in the surface proteome of rat cortical neurons and astrocytes. Focusing on the glutamate transporters, SLC1A1 and SLC1A3, we have validated that SNX27-Retromer is required for their trafficking, with SNX27-Retromer suppression in astrocytes leading to a loss of glutamate uptake. C_FIG

molecular biology↗

bioRxiv2026

The Vagus Nerve conducts viable translocation of gut flora to the lungs that impacts interstitial lung disease severity in mice

Communication between gut microbiota and extraintestinal organs is increasingly recognized, yet elucidation of relevant translocation mechanism(s) remains enigmatic. Vagus neuroanatomy and reports of vagal protein transfer to extraintestinal organs suggest that this "superhighway" could translocate bacteria. Here we explore whether the vagus superhighway can translocate bacteria to extraintestinal organs. Gavage of green fluorescent protein-expressing Escherichia coli (GFP-E. coli) into germ-free (GF) or specific-pathogen free (SPF) C57BL/6 mice yielded high bacillary loads in the stomach and lungs, followed by the heart, stool and peripheral muscles, despite negative blood cultures. Notably, confocal microscopy and culture revealed GFP-E. coli within the vagus nerve within five minutes of gavage suggesting rapid translocation. Metagenomic analysis of stool, lung, heart, vagus nerve, and muscle from non-gavaged SPF mice demonstrated significant microbial overlap, supporting that bacterial translocation occurs despite the presence of endogenous microflora. Remarkably, subdiaphragmatic vagotomy performed prior to GFP-E. coli gavage resulted in marked reductions of bacterial transduction in the lungs and other extraintestinal organs, except muscle. Furthermore, vagotomy significantly reduced lung fibrosis in SPF mice following intranasal bleomycin administration. In lung cancer patients undergoing lobectomy, vagotomy inhibited postsurgical reductions in forced vital capacity. These findings identify the vagus nerve as a literal gut-lung axis, facilitating viable bacterial translocation and influencing lung severity.

microbiology↗

bioRxiv2026

Novel visuomotor adaptation paradigm reveals a role of visual cortex in the plasticity of innate behaviors in mice

A long-standing hypothesis in sensory neuroscience suggests that the evolutionary expansion of cortex in mammals may contribute to sensory-dependent adaptation by acting on subcortical pathways that drive innate behavior. However, direct experimental evidence is lacking. Taking the visual system as a model, it is known that there is significant interaction between the evolutionarily conserved Superior Colliculus (SC) and the comparatively modern Visual Cortex (VC), key structures in the mammalian visual system. In the SC, local alignment is established between a retinotopic map of the visual field and a map of orienting movement vectors during development and drives accurate visually guided orienting behavior throughout an organisms lifespan. Interestingly mammals, like humans and non-human primates, readily adapt to altered visual experiences, while evolutionarily older vertebrates, like amphibians, lack this behavioral plasticity. To address this outstanding question, we have developed a novel behavioral paradigm for inducing visuomotor adaptation in freely moving mice that is analogous to paradigms utilized in primates. Our paradigm combines a visually guided orienting task and a novel mouse prism goggle system to shift the visual field. Using this paradigm, we demonstrate for the first time that mice gradually adapt to a chronic shift of their full visual field, suggesting this type of behavioral plasticity is conserved across mammalian species. Furthermore, we show that lesioning primary visual cortex (V1) prior to shifting the visual field disrupts normal visuomotor adaptation, suggesting that VC may play a generative role in the plasticity of fundamental visually guided behaviors. These findings lend support to the hypothesis that a particular evolutionary benefit of sensory cortex is the allowance for experience-dependent behavioral plasticity.

neuroscience↗

bioRxiv2026

YdbL directly modulates YdbH-YnbE bridge formation to maintain Escherichia coli outer membrane homeostasis

Gram-negative bacteria pose a threat to global healthcare mainly because their outer membrane (OM) provides an intrinsic barrier to many antimicrobials. Key to this barrier function is the asymmetric structure of the OM, with phospholipids constituting the inner leaflet and lipopolysaccharides the outer leaflet. Although the mechanism of phospholipid transport between the inner membrane (IM) and OM remains poorly understood, recent studies implicate TamB, YhdP, and YdbH as functionally redundant proteins mediating this process in Escherichia coli. Accordingly, collective loss of these three paralogs is lethal and any one of them is sufficient for growth. YdbH is anchored to the IM and its periplasmic repeating {beta}-sheet groove domain interacts with the OM lipoprotein YnbE via {beta}-strand augmentation to form an intermembrane bridge. Additionally, YnbE multimerizes, and the periplasmic protein YdbL is proposed to modulate YnbE multimerization to facilitate its stacking on the C-terminus of YdbH. Here, we demonstrate that excess YdbL specifically inhibits the function of the YdbH-YnbE complex since overexpression of ydbL causes lethality in the {Delta}yhdP {Delta}tamB double mutant but the presence of both ydbH and ynbE in trans abrogates this lethality. We resolve high-resolution structural data for YdbL and ascertain its interaction site with the YnbE C-terminal -helix, with residues mediating this interface highly conserved and critical for YdbL function. Finally, we show that YdbL is protected from degradation by the protease DegP when complexed with YnbE. Overall, our data supports a model in which YdbL ensures proper YdbH-YnbE intermembrane bridge formation by directly interacting with YnbE.

microbiology↗

bioRxiv2026

Repeated and widespread introduction of a mosquito-borne virus, but wildlife impact remains localised in urban area

Mosquito-borne viruses are emerging in new regions with increasing regularity. Shifting climatic envelopes, especially in temperate regions, and altered enzootic cycles are changing likelihoods of persistence, meaning new approaches are required to predict and monitor establishment. Usutu virus (USUV) is a mosquito-borne viral zoonosis, which was first recorded in the United Kingdom in wild birds and mosquitoes in 2020. By developing a multidisciplinary approach, incorporating enhanced passive and active surveillance of wild birds, we discovered previously unrecorded introductions and identified USUV persistence and geographic expansion. By combining molecular and serological testing with citizen science derived datasets, we show an associated marked decline in a common, widespread, and highly susceptible host species (Eurasian Blackbird, Turdus merula). However, the clearest continuous signal of host population decline remains localised to a large urban area, despite the much wider virus distribution. This may be a consequence of an urban heat island effect and associated increase in length of the mosquito active season. Our results indicate that the establishment and impact of future mosquito-borne pathogens in temperate zones, anticipated under climate change, may first be most apparent in urban areas. Consequently, enhanced surveillance efforts in urban areas could provide an efficient mechanism for detecting novel pathogen emergence. The epidemiology of emerging vector-borne diseases, especially in temperate areas, depends on the interplay between climate, land-use and available hosts; therefore, considering each in isolation will not be sufficient to reliably inform surveillance or response planning.

ecology↗

bioRxiv2026

Dysregulation of xenobiotic metabolism and mitochondrial dysfunction exacerbate acetaminophen-induced hepatotoxicity in human antigen R-deficient male mice

Acetaminophen (APAP) overdose is a leading cause of acute liver failure worldwide. The RNA-binding protein Human antigen R (HuR) is a multifunctional post-transcriptional regulator that plays a pivotal role in cellular stress responses, including those triggered by APAP toxicity. This study investigated the mechanisms by which HuR protects against APAP-induced hepatotoxicity in male mice. Hepatocyte-specific HuR-deficient (HuRHep-/-) male mice on a C57BL/6N background and wild-type (WT) littermates were treated with 200 mg/kg APAP, and liver tissues were collected at 2, 6, and 24 hours post-treatment. APAP administration increased hepatic HuR mRNA expression and induced HuR cleavage and the formation of a higher-molecular weight HuR-immunoreactive band, with the latter two correlating with injury severity. Compared with WT controls, HuRHep-/- mice exhibited markedly increased susceptibility to hepatotoxicity at both 2 and 6 hours. Metabolite profiling revealed altered APAP metabolism and reduced glutathione S-transferase (Gst) expression in HuRHep-/- livers, consistent with impaired APAP detoxification and increased APAP-protein adduct formation. Fourier-transform infrared (FTIR) spectroscopy further identified early biochemical differences between WT and HuRHep-/- livers as early as 2 hours after APAP exposure. Additionally, HuR deficiency resulted in pronounced mitochondrial structural abnormalities and dysfunction at 2 and 6 hours, accompanied by reduced expression of the mitochondrial fission and fusion proteins Drp1 and Mfn2, increased mitochondrial protein release, and enhanced hepatocyte death. Although pro-inflammatory cytokine levels were elevated in HuRHep-/- mice relative to WT controls at 24 hours, hepatocyte proliferation was similarly blunted in both genotypes, consistent with severe liver injury and delayed recovery. Collectively, these findings identify hepatocyte HuR as a critical regulator of xenobiotic metabolism and mitochondrial integrity and establish its essential role in early protection against APAP-induced hepatotoxicity in male mice.

pharmacology and toxicology↗

bioRxiv2025

Hippocampal CA3 Nex/Neurod6+ neuron-specific TNFR2 alleviates chronic neuropathic pain by sex-dependently engaging opioid and endocannabinoid pathways

Chronic neuropathic pain (CNP) develops as a result of persistent neuroinflammation and maladaptive synaptic plasticity in the central nervous system following nerve injury. While tumor necrosis factor receptor 2 (TNFR2) signaling has been extensively studied in pain resolution, the expression of this receptor on specific neuronal populations and molecular pathways involved in spontaneous pain recovery still remains poorly defined. In this study, we investigated the role of TNFR2 signaling within hippocampal Nex/Neurod6 pyramidal neurons in promoting recovery from chronic constriction injury (CCI), a well-established rodent model of neuropathic pain. To achieve neuron-specific deletion of TNFR2, we generated tamoxifen-inducible conditional knockout mice (NexCreERT2:TNFR2F/F). We demonstrate that knocking out TNFR2 from Nex neurons prevents spontaneous pain recovery in both males and females. Thus, establishing that a supraspinal TNFR2 neuroimmune axis is necessary for pain recovery. Exogenous administration of a TNFR2 agonist at 7, 10, and 13 dpi (i.p.) significantly improved mechanical withdrawal thresholds in both sexes of wild-type mice but did not alleviate pain in Nex-specific TNFR2 knockouts, indicating that neuronal TNFR2 expression is required for TNFR2-mediated analgesia. Bulk RNA sequencing of hippocampal tissue collected at six weeks after CCI revealed that TNFR2 activation upregulates genes such as Pomc, involved in the opioid pathway, and oleoyl-ACP-hydrolase (OLAH), involved in the endocannabinoid pathway. Consistent with these findings, immunostaining and Western blot analyses showed that TNFR2 agonism restored cornu ammonis (CA3) region POMC and {beta}-endorphin protein levels that were otherwise suppressed after CCI. Behavioral experiment demonstrated that systemic blockade of the {micro}-opioid receptor with naltrexone (administered daily from 7-21 dpi (s.c.)) completely prevented TNFR2-mediated pain recovery in males but only partially in females. In contrast, inhibition of cannabinoid 1 receptor (CB1R) signaling with AM251 (administered at 7, 14, and 21 dpi (i.p.)) abolished TNFR2-driven analgesia in both sexes. Together, these results reveal that hippocampal TNFR2 signaling in Nex/Neurod6 neurons is critical in recovery from chronic neuropathic pain. TNFR2 activation promotes analgesia by engaging endogenous {beta}-endorphin/{micro}-opioid and endocannabinoid pathways in a sex-dependent manner, establishing TNFR2 agonism as a promising non-addictive therapeutic approach for chronic pain resolution. SignificanceChronic neuropathic pain (CNP) results from persistent neuroimmune signaling and is driven by maladaptive circuit plasticity. Due to the complexity of factors contributing to CNP, it often leaves patients with few treatment options, which, unfortunately, are either temporary or might be addictive. We have characterized a novel supraspinal mechanism through which tumor necrosis factor receptor 2 (TNFR2) signaling, specifically in hippocampal Neurod6/Nex+ expressing pyramidal neurons, is necessary for pain recovery following nerve injury. Pharmacological activation of TNFR2 in these neurons alleviates pain by engaging both endogenous opioid and endocannabinoid signaling pathways. We specifically demonstrate that TNFR2 agonism upregulates proopiomelanocortin (POMC) expression and {beta}-endorphin levels in the hippocampus. We further identify that pharmacological inhibition of either the -opioid receptor or cannabinoid 1 (CB1) receptor is sufficient to impair the effectiveness of TNFR2 agonist mediated pain resolution. Our findings thus uncover a novel neuroimmune mechanism where the TNFR2 agonist, exogenously activating the pro-resolving TNFR2, mitigates CNP by releasing endogenous pain neuromodulators. Here, we highlight that TNFR2 agonism could serve as a non-addictive therapeutic strategy for the resolution of chronic neuropathic pain.

pharmacology and toxicology↗

bioRxiv2025

ER oxidoreductin-1α and unfolded protein response as sex-dependent drivers of cardiorenal dysfunction in experimental autoimmune encephalomyelitis

BackgroundMultiple sclerosis (MS) is associated with increased cardiovascular and renal morbidity, but mechanisms linking CNS autoimmunity to peripheral organ injury remain poorly defined. We tested the hypothesis that experimental autoimmune encephalomyelitis (EAE) induces cardiorenal dysfunction via sex-specific dysregulation of endoplasmic reticulum (ER) oxidoreductases and unfolded protein response (UPR) signaling. MethodsAdult female and male C57BL/6J mice [10-12 weeks] and IRE1C148S knock-in mice underwent non-pertussis toxin EAE (nPTX-EAE) induced with 100{micro}g MOG35-55 in CFA and 200{micro}g heat-inactivated MTB with a booster at 7 days. Controls received all components except MOG. Motor scoring was done daily and EN460 (ERO1 inhibitor, 10 mg/kg IP) was given twice weekly beginning at 10DPI. Echocardiography and renal Doppler (Vevo 2100) were performed at 36-38DPI with primary outcomes of LV systolic/diastolic function and renal perfusion with tissue collected at 40DPI. LV and kidney were analyzed via western blot for ERO1, PDIA1, Prdx4, 4HNE, and BiP. Data are expressed as mean {+/-} SEM with two-way ANOVA/Tukeys post hoc or Mann Whitney test performed and outliers identified by ROUT (Q=1%). ResultsSixty-seven percent of immunized mice developed motor deficits. At 36-38DPI, EAE reduced ejection fraction and fractional shortening while increasing IVCT, IVRT, and myocardial performance index without hypertrophy. Renal resistive index increased and end-diastolic velocity decreased in addition to reduced Bowmans space at 40DPI. Females showed upregulated LV ERO1 and 4HNE while males exhibited reduced PDI and Prdx4 paired with elevated BiP. EN460 attenuated cardiac and renal dysfunction and lowered LV ERO1/4HNE in females, but not males. IRE1C148S mitigated cardiac dysfunction in males and restore renal indices in both sexes. ConclusionsnPTX-EAE causes clinically relevant, sex-specific cardiorenal dysfunction linked to distinct ER stress/UPR alterations. ERO1 inhibition protects females, whereas enhanced IRE1 activity protects males and kidneys across sexes, supporting sex-specific ER stress-targeted therapies for MS-associated cardiorenal disease.

molecular biology↗

bioRxiv2025

Phosphodiesterase type 1 regulates adenosine 2A receptor-associated cAMP signaling at the plasma membrane to increase myocardial contractility

BACKGROUNDPhosphodiesterase type 1 (PDE1) inhibition exerts inodilatory effects in pre-clinical models and human heart failure patients with reduced ejection fraction (HFrEF). PDE1 hydrolyzes cyclic nucleotide cAMP in a soluble but not microsomal fraction of the human myocardium. PDE1 may exert domain-specific effects, but the mechanism whereby PDE1 compartmentalization induces an inotropic change remains unknown. We sought to elucidate PDE1 regulation of cAMP and contractility. METHODSPharmacologic modulators of PDEs or G-protein coupled receptors (GPCRs) were used to study PDE1 signaling mechanisms in healthy and failing guinea pig hearts. Tissue fractionation examined the localization of different PDE types. Live cell imaging experiments assessed cytosolic and sarcolemmal membrane cAMP level ([cAMP]) and protein kinase A (PKA) activity changes in cells transduced with Forster resonance energy transfer (FRET) biosensors. Sarcomere length and intracellular calcium changes monitored contractile changes in electrically paced cells. Coronary flow and left ventricular (LV) developed pressure were measured in ex vivo Langendorff perfusion heart studies. RESULTSPDE1 isoforms were found not only in the soluble, but also in the microsomal fractions of the guinea pig heart. PDE1 hydrolysis of cAMP was greater at the sarcolemma compared to the cytosol. PDE1 specifically regulated a pool of cAMP associated with the Gs protein coupled receptor adenosine 2A receptor (A2AR) at the sarcolemma, without activating PKA. A2AR/PDE1 regulation induced positive inotropic and lusitropic changes in healthy and failing guinea pig cardiomyocytes and in the myocardium ex vivo. CONCLUSIONSPDE1 is the major regulator of cAMP pools generated by A2AR activation at the sarcolemma. Functionally, this regulation induces inotropic and lusitropic effects in cardiomyocytes and at the whole organ level. Thus, PDE1 is compartmentalized at the membrane with A2AR, and this regulation determines cardiomyocyte contractility in healthy and failing hearts.

physiology↗

bioRxiv2025

Pupation substrate and prepupal handling affect eclosion rate, timing, and adult morphology in black soldier flies (Hermetia illucens; Diptera: Stratiomyidae)

On farms, the conditions experienced by black soldier fly (BSF) prepupae may impact their development and survival, altering production goals by changing the fitness of breeding adults. Few studies have addressed the impact of environmental variables (such as substrate type or moisture content), or stressors like handling, on the development and survival of BSF as they transition from prepupae through adulthood. This study examined the effects of pupation substrate (corn cob grits, potting soil, vermiculite, wood chips, and frass), moisture content (20%, 60%, and 100%), and handling during the prepupal period (daily handling, no handling) on eclosion rate and timing, morphology (mass, head width, thorax length), and abdominal window fullness of adult BSF. Handling delayed adult emergence by over three days, reduced eclosion rates by 30.6%, reduced head width and wet mass in adult males, and reduced window fullness and head width in adult females. Frass resulted in the lowest eclosion rate (72.1 {+/-} 2.4%) while corn cob grits (82.2 {+/-} 2.3%) and wood chips (81.5 {+/-} 2.2%) had the highest. Wood chips also resulted in the highest wet and dry mass, head width, and thorax length for adult males and females. Wood chips may be the best pupation substrate for BSF as it enhances body size and has a good eclosion rate. Significant prepupal handling delays adult emergence, reduces eclosion/survival rates, and reduces adult body size; however, more research is necessary to determine if the less chronic handling regimes that are likely present on farms produce similar effects.

zoology↗

bioRxiv2025

Microtubule curling as an efficient readout to uncover fundamental concepts of axonal cell biology

Nerve fibres (aka axons) are the slender, up-to-meter-long processes of nerve cells that wire nervous systems. These delicate structures must survive for an organisms lifetime, making them prime lesion sites in neurodegeneration. Their long-term maintenance requires the homeostasis of complex local cell biology upheld by motor protein-driven transport along microtubule bundles that run uninterrupted along axons. To gain an understanding of axonal homeostasis, we report and discuss here the functional loss of 105 genes from a wide range of cell biological processes using a standardised Drosophila primary neuron system. [~]40% of these gene deficiencies caused microtubule bundle disturbances referred to as microtubule-curling, which we use as an indicator of axonal atrophy. Our live imaging showed that microtubule-curling initiates in areas where axons widen, such as areas close to the soma, branch points or growth cones. In wild-type neurons, any initiated curling was contained, but it persisted as growing footprints in mutant curl-promoting conditions. Closer analyses of 20 curl-promoting conditions suggested a general classification into two groups: mutations affecting axonal physiology cause ROS-mediated microtubule-curling, whereas mutations causing motor hyperactivation or affecting microtubule-regulating proteins cause structurally induced ROS-independent curling. As will be discussed, our data provide consistent support for the previously proposed dependency cycle of local axon homeostasis model which can explain the long-standing conundrum that genes from a wide range of cell biological processes often have mutational links to the same class of inherited neurodegenerative disease.

cell biology↗

bioRxiv2025

The gut microbiota metabolite isovalerate enhances the epithelial barrier function in cell monolayers derived from porcine ileum organoids

The gut microbiota produces numerous metabolites that influence the epithelial barrier function. Bacterial catabolism of amino acids produces a wide variety of metabolites whose effects on the intestinal epithelium remain to be fully identified. In this study, we investigated the effects of amino acid derived metabolites (isovalerate, isobutyrate, 2-methylbutyrate, 5-aminovalerate, cadaverine, putrescine, and tryptamine) in cell monolayers derived from porcine ileum organoids. Our results show that the leucine-derived branched-chain fatty acid (BCFA) isovalerate improved the epithelial barrier function, as assessed by transepithelial electrical resistance measurement and permeability assay. Isovalerate upregulated the expression of genes involved in innate immunity, markers of absorptive cells and enteroendocrine cells while reducing the expression of the stem cells and mucus related genes. Most of the effects of isovalerate on epithelial cells were also observed with the bacterial metabolite butyrate, an inhibitor of the epigenetic enzymes histone deacetylases (HDAC). Furthermore, the structurally unrelated HDAC inhibitor trichostatin A improved epithelial barrier function and upregulated SLPI gene expression, as observed with isovalerate and butyrate. Isovalerate also upregulated the gene expression of antioxidant enzymes and this effect was not observed with butyrate. Interestingly, the other two BCFAs isobutyrate and 2-methylbutyrate did not replicate the effects of isovalerate, suggesting that the carbon chain structure of isovalerate mediates its effect. In contrast, we found that all three BCFAs were able to cross the epithelial cell monolayer derived from porcine ileum organoids from the apical to the basal side. Overall, our in vitro results suggest that targeting the bacterial production of isovalerate may be useful to promote gut health. In this perspective, we performed an in silico analysis that identified species belonging to dominant gut microbiota genera such as Prevotella, Blautia, Christensenella, Clostridium, and Ruminococcus, as potential producers of BCFAs through the PorA enzymatic pathway.

cell biology↗

bioRxiv2025

Different mechanisms link gain and loss of kinesin functions to axonal degeneration

Axons are the slender, often meter-long projections of neurons that form the biological cables wiring our bodies. Most of these delicate structures must survive for an organisms lifetime, meaning up to a century in humans. Long-term maintenance and sustained functionality of axons requires motor protein-driven transport distributing life-sustaining materials and organelles to places of need. It seems therefore plausible that loss of motor function would cause axon degeneration; however, also gain-of-function conditions were linked to disorders including motor neuron disease or spastic paraplegia. To understand this phenomenon, we studied [~]40 genetic manipulations of motor proteins, cargo linkers and regulators of reactive oxygen species in one standardised Drosophila primary neuron system. Using axonal microtubule bundle organisation as a relevant readout reflecting the state of axon integrity, we found that losses of Dynein heavy chain, KIF1A/Unc-104 and KIF5/Kinesin heavy chain (Khc) all cause bundle disintegration in the form of chaotically curled microtubules. Detailed functional studies of Khc and its adaptor proteins revealed that losses of mitochondrial or lysosomal transport cause ROS dyshomeostasis, which is a microtubule-curl-inducing condition in fly and mouse neurons alike. We find that hyper-activated Khc induces the same microtubule curling phenotype, not through ROS but likely more directly through enhanced mechanical forces. Studies with loss of Unc-104 or KIFBP and expression of an ALS-linked mutant form of the human Khc orthologue KIF5A suggest that loss or hyperactivation of different types of transport motors cause MT curling as a shared feature. We discuss a model which can explain our findings and their relevance for understanding motor-linked neurodegeneration.

neuroscience↗

bioRxiv2024

A single-cell atlas of transcriptome changes in the intestinal epithelium at the suckling-to-weaning transition

The suckling-to-weaning dietary transition is a key step in mammalian intestinal development. However, the relative contributions of genetically wired and nutritional factors in this maturation process remain to be elucidated. Moreover, the cellular diversity of the intestinal epithelium has been overlooked in this context. The aim of our study was to identify the transcriptome changes induced in each cell type of the intestinal epithelium at the onset of solid food ingestion. We compared the single-cell transcriptome of epithelial cells isolated from the caecum of age-matched littermate suckling rabbits ingesting or not solid food. Our dataset provides the first single-cell atlas of the rabbit intestinal epithelium and highlights the interest of the rabbit as a model for studying BEST4+ epithelial cells, which are absent in mice. Solid food ingestion induced extensive transcriptome changes in each epithelial cell type, with the most pronounced changes noted in absorptive and BEST4+ cells. Some of the effects of solid food introduction were common to most epithelial cell types, such as the upregulation of ALDH1A1, which encodes for a vitamin A processing enzyme. Solid food ingestion remodeled epithelial defenses systems, as observed by the increased expression of interferon-stimulated genes in mature absorptive and BEST4+ cells. Solid food also upregulated the gene expression of the immunoglobulin transporter PIGR, specifically in cells located at the base of epithelial crypts and in goblet cells. In addition, solid food triggered epithelial differentiation, which was associated with modification of the expression of genes involved in handling of amino acids, lipids and bile acids, as well as changes in hormone expression by enteroendocrine cells. These cell type-specific transcriptome modifications induced by solid food ingestion coincided with changes in microbiota composition and metabolic activity, which may contribute to epithelial maturation. Overall, our work provides a single-cell atlas of the transcriptome changes induced in the intestinal epithelium at the suckling-to-weaning transition.

physiology↗

bioRxiv2024

Early NK-cell and T-cell dysfunction marks progression to severe dengue in patients with obesity and healthy weight

Dengue is a mosquito-borne virus infection affecting half of the worlds population for which therapies are lacking. The role of T and NK-cells in protection/immunopathogenesis remains unclear for dengue. We performed a longitudinal phenotypic, functional and transcriptional analyses of T and NK-cells in 124 dengue patients using flow cytometry and single-cell RNA-sequencing. We show that T/NK-cell signatures early in infection discriminate patients who will progress to severe dengue (SD) from those who do not. In patients with overweight/obesity these signatures are exacerbated compared to healthy weight patients, supporting their increased susceptibility to SD. In SD, CD4+/CD8+ T-cells and NK-cells display increased co-inhibitory receptor expression and decreased cytotoxic capacity compared to non-SD. Furthermore, type-I Interferon signalling is downregulated in SD, suggesting defective virus-sensing mechanisms may underlie NK/T-cell dysfunction. We propose that dysfunctional "professional killer" T/NK-cells underpin dengue pathogenesis. Our findings pave the way for the evaluation of immunomodulatory therapies for dengue.

immunology↗

bioRxiv2024

Proteomic and Metabolomic Profiling of Archaeal Extracellular Vesicles from the Human Gut

One potential mechanism for microbiome-host, and microbiome constituents interaction and communication involves extracellular vesicles (EVs). Here, for the first time, we report the capability of two M. smithii strains (ALI and GRAZ-2), Candidatus M. intestini, and Methanosphaera stadtmanae, as underrepresented components of the gut microbiome, to produce EVs. Interesting, size, morphology, and composition of AEVs were comparable to bacterial EVs, as indicated by ultrastructure, composition, proteomic and metabolomic analyses; however, EVs were substantially less prevalent in the studied Archaea. When looking at the proteomics more precisely, although AEVs from M. smithii ALI and M. intestini were found to be carrying unique proteins (n=135 and n=30, respectively), the shared proteins in AEVs within this genus (n=229), were mostly adhesins(/like) proteins, or proteins with IG-like domains. One remarkable observation was the uptake of AEVs obtained from Methanosphaera stadtmanae and the studied Methanobrevibacter species by human monocytes and the subsequent IL-8 secretion.

microbiology↗